Are there any differences between the JPG preview and the Raw file if you view them both uncropped. I know some cameras generate a JPG preview that is slightly smaller than the Raw file by some number of pixels, and that may result in what you're seeing. Photo Mechanic will write the crop to the metadata based on the pixels of the JPG and if the Raw has different dimensions, it can appear shifted. (Just guessing without seeing your screenshots)
Mick
